MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots[W]
Identifieur interne : 000C86 ( Pmc/Corpus ); précédent : 000C85; suivant : 000C87MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots[W]
Auteurs : Rui Xia ; Blake C. Meyers ; Zhongchi Liu ; Eric P. Beers ; Songqing Ye ; Zongrang LiuSource :
- The Plant Cell [ 1040-4651 ] ; 2013.
Abstract
This work shows the conservation in eudicots of a miRNA-TAS-PPR-siRNA pathway characterized by a set of 22-nucleotide miRNAs that trigger secondary siRNAs using distinct mechanistic strategies. This super-miR7122 family of miRNAs includes miR173 and originates from miR390, emerging via gene duplication and neofunctionalization, which involved yet another miRNA superfamily (super-miR4376).
Url:
DOI: 10.1105/tpc.113.110957
PubMed: 23695981
PubMed Central: 3694692
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</title>
<author><name sortKey="Xia, Rui" sort="Xia, Rui" uniqKey="Xia R" first="Rui" last="Xia">Rui Xia</name>
<affiliation><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff2">Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, West Virginia 25430</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff3">Alson H. Smith Agricultural Research and Extension Center, Department of Horticulture, Virginia Polytechnic Institute and State University, Winchester, Virginia 22602</nlm:aff>
</affiliation>
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<author><name sortKey="Meyers, Blake C" sort="Meyers, Blake C" uniqKey="Meyers B" first="Blake C." last="Meyers">Blake C. Meyers</name>
<affiliation><nlm:aff id="aff4">Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Liu, Zhongchi" sort="Liu, Zhongchi" uniqKey="Liu Z" first="Zhongchi" last="Liu">Zhongchi Liu</name>
<affiliation><nlm:aff id="aff5">Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Beers, Eric P" sort="Beers, Eric P" uniqKey="Beers E" first="Eric P." last="Beers">Eric P. Beers</name>
<affiliation><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ye, Songqing" sort="Ye, Songqing" uniqKey="Ye S" first="Songqing" last="Ye">Songqing Ye</name>
<affiliation><nlm:aff id="aff5">Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Liu, Zongrang" sort="Liu, Zongrang" uniqKey="Liu Z" first="Zongrang" last="Liu">Zongrang Liu</name>
<affiliation><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff2">Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, West Virginia 25430</nlm:aff>
</affiliation>
</author>
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<idno type="pmc">3694692</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694692</idno>
<idno type="RBID">PMC:3694692</idno>
<idno type="doi">10.1105/tpc.113.110957</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots<xref ref-type="author-notes" rid="fn1"><sup>[W]</sup>
</xref>
</title>
<author><name sortKey="Xia, Rui" sort="Xia, Rui" uniqKey="Xia R" first="Rui" last="Xia">Rui Xia</name>
<affiliation><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff2">Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, West Virginia 25430</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff3">Alson H. Smith Agricultural Research and Extension Center, Department of Horticulture, Virginia Polytechnic Institute and State University, Winchester, Virginia 22602</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Meyers, Blake C" sort="Meyers, Blake C" uniqKey="Meyers B" first="Blake C." last="Meyers">Blake C. Meyers</name>
<affiliation><nlm:aff id="aff4">Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Liu, Zhongchi" sort="Liu, Zhongchi" uniqKey="Liu Z" first="Zhongchi" last="Liu">Zhongchi Liu</name>
<affiliation><nlm:aff id="aff5">Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Beers, Eric P" sort="Beers, Eric P" uniqKey="Beers E" first="Eric P." last="Beers">Eric P. Beers</name>
<affiliation><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ye, Songqing" sort="Ye, Songqing" uniqKey="Ye S" first="Songqing" last="Ye">Songqing Ye</name>
<affiliation><nlm:aff id="aff5">Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Liu, Zongrang" sort="Liu, Zongrang" uniqKey="Liu Z" first="Zongrang" last="Liu">Zongrang Liu</name>
<affiliation><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff>
</affiliation>
<affiliation><nlm:aff id="aff2">Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, West Virginia 25430</nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">The Plant Cell</title>
<idno type="ISSN">1040-4651</idno>
<idno type="eISSN">1532-298X</idno>
<imprint><date when="2013">2013</date>
</imprint>
</series>
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<front><div type="abstract" xml:lang="en"><p>This work shows the conservation in eudicots of a miRNA-TAS-PPR-siRNA pathway characterized by a set of 22-nucleotide miRNAs that trigger secondary siRNAs using distinct mechanistic strategies. This super-miR7122 family of miRNAs includes miR173 and originates from miR390, emerging via gene duplication and neofunctionalization, which involved yet another miRNA superfamily (super-miR4376).</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant Cell</journal-id>
<journal-id journal-id-type="iso-abbrev">Plant Cell</journal-id>
<journal-id journal-id-type="hwp">plantcell</journal-id>
<journal-id journal-id-type="publisher-id">aspb</journal-id>
<journal-title-group><journal-title>The Plant Cell</journal-title>
</journal-title-group>
<issn pub-type="ppub">1040-4651</issn>
<issn pub-type="epub">1532-298X</issn>
<publisher><publisher-name>American Society of Plant Biologists</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23695981</article-id>
<article-id pub-id-type="pmc">3694692</article-id>
<article-id pub-id-type="publisher-id">110957</article-id>
<article-id pub-id-type="doi">10.1105/tpc.113.110957</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Articles</subject>
</subj-group>
</article-categories>
<title-group><article-title>MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots<xref ref-type="author-notes" rid="fn1"><sup>[W]</sup>
</xref>
</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Xia</surname>
<given-names>Rui</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
<xref ref-type="aff" rid="aff3"><sup>c</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Meyers</surname>
<given-names>Blake C.</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>d</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Liu</surname>
<given-names>Zhongchi</given-names>
</name>
<xref ref-type="aff" rid="aff5"><sup>e</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Beers</surname>
<given-names>Eric P.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ye</surname>
<given-names>Songqing</given-names>
</name>
<xref ref-type="aff" rid="aff5"><sup>e</sup>
</xref>
<xref ref-type="author-notes" rid="afn2"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Liu</surname>
<given-names>Zongrang</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>2</sup>
</xref>
</contrib>
<aff id="aff1"><label>a</label>
Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</aff>
<aff id="aff2"><label>b</label>
Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, West Virginia 25430</aff>
<aff id="aff3"><label>c</label>
Alson H. Smith Agricultural Research and Extension Center, Department of Horticulture, Virginia Polytechnic Institute and State University, Winchester, Virginia 22602</aff>
<aff id="aff4"><label>d</label>
Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717</aff>
<aff id="aff5"><label>e</label>
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742</aff>
</contrib-group>
<author-notes><corresp id="cor1"><label>2</label>
Address correspondence to <email>zongrang.liu@ars.usda.gov</email>
.</corresp>
<fn id="afn2" fn-type="present-address"><label>1</label>
<p>Current address: Division of Plant Sciences, University of Missouri, Columbia, MO 65211.</p>
</fn>
<fn id="afn1"><p>The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (<ext-link ext-link-type="uri" xlink:href="http://www.plantcell.org">www.plantcell.org</ext-link>
) is: Zongrang Liu (<email>zongrang.liu@ars.usda.gov</email>
).</p>
</fn>
<fn id="fn1"><label>[W]</label>
<p>Online version contains Web-only data.</p>
</fn>
<fn><p><ext-link ext-link-type="uri" xlink:href="http://www.plantcell.org/cgi/doi/10.1105/tpc.113.110957">www.plantcell.org/cgi/doi/10.1105/tpc.113.110957</ext-link>
</p>
</fn>
</author-notes>
<pmc-comment>Fake ppub date generated by PMC from publisher
pub-date/@pub-type='epub-ppub' </pmc-comment>
<pub-date pub-type="ppub"><month>5</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>21</day>
<month>5</month>
<year>2013</year>
</pub-date>
<volume>25</volume>
<issue>5</issue>
<fpage>1555</fpage>
<lpage>1572</lpage>
<history><date date-type="received"><day>25</day>
<month>2</month>
<year>2013</year>
</date>
<date date-type="rev-recd"><day>23</day>
<month>4</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>02</day>
<month>5</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>© 2013 American Society of Plant Biologists. All rights reserved.</copyright-statement>
<copyright-year>2013</copyright-year>
</permissions>
<self-uri xlink:role="icon" xlink:type="simple" xlink:href="PC_110957_ic1.gif"></self-uri>
<abstract abstract-type="precis"><p>This work shows the conservation in eudicots of a miRNA-TAS-PPR-siRNA pathway characterized by a set of 22-nucleotide miRNAs that trigger secondary siRNAs using distinct mechanistic strategies. This super-miR7122 family of miRNAs includes miR173 and originates from miR390, emerging via gene duplication and neofunctionalization, which involved yet another miRNA superfamily (super-miR4376).</p>
</abstract>
<abstract><p><italic>Trans</italic>
-acting small interfering RNAs (<xref ref-type="def" rid="def4">tasiRNAs</xref>
) are a major class of small RNAs performing essential biological functions in plants. The first reported <xref ref-type="def" rid="def4">tasiRNA</xref>
pathway, that of miR173-<italic>TAS1/2</italic>
, produces <xref ref-type="def" rid="def4">tasiRNAs</xref>
regulating a set of pentatricopeptide repeat (<italic>PPR</italic>
) genes and has been characterized only in <italic>Arabidopsis thaliana</italic>
to date. Here, we demonstrate that the microRNA (<xref ref-type="def" rid="def2">miRNA</xref>
)-<italic>trans</italic>
-acting small interfering RNA gene (<italic>TAS</italic>
)-pentatricopeptide repeat-containing gene (<italic>PPR</italic>
)-small interfering RNA pathway is a highly dynamic and widespread feature of eudicots. Nine eudicot plants, representing six different plant families, have evolved similar <xref ref-type="def" rid="def4">tasiRNA</xref>
pathways to initiate phased small interfering RNA (<xref ref-type="def" rid="def5">phasiRNA</xref>
) production from <italic>PPR</italic>
genes. The <italic>PPR</italic>
<xref ref-type="def" rid="def5">phasiRNA</xref>
production is triggered by different 22-nucleotide <xref ref-type="def" rid="def2">miRNAs</xref>
, including miR7122, miR1509, and fve-PPRtri1/2, and through distinct mechanistic strategies exploiting <xref ref-type="def" rid="def2">miRNA</xref>
direct targeting or indirect targeting through <italic>TAS</italic>
-like genes (<italic>TASL</italic>
), one-hit or two-hit, or even two layers of <xref ref-type="def" rid="def4">tasiRNA</xref>
–<italic>TASL</italic>
interactions. Intriguingly, although those <xref ref-type="def" rid="def2">miRNA</xref>
triggers display high sequence divergence caused by the occurrence of frequent point mutations and splicing shifts, their corresponding <italic>MIRNA</italic>
genes show pronounced identity to the <italic>Arabidopsis MIR173</italic>
, implying a common origin of this group of <xref ref-type="def" rid="def2">miRNAs</xref>
(super-miR7122). Further analyses reveal that super-miR7122 may have evolved from a newly defined miR4376 superfamily, which probably originated from the widely conserved miR390. The elucidation of this evolutionary path expands our understanding of the course of <xref ref-type="def" rid="def2">miRNA</xref>
evolution, especially for relatively conserved <xref ref-type="def" rid="def2">miRNA</xref>
families.</p>
</abstract>
<counts><page-count count="18"></page-count>
</counts>
</article-meta>
<notes><glossary><title>Glossary</title>
<def-list><def-item><term id="term1">sRNA</term>
<def id="def1"><p>small RNA</p>
</def>
</def-item>
<def-item><term id="term2">miRNA</term>
<def id="def2"><p>microRNA</p>
</def>
</def-item>
<def-item><term id="term3">siRNA</term>
<def id="def3"><p>small interfering RNA</p>
</def>
</def-item>
<def-item><term id="term4">tasiRNA</term>
<def id="def4"><p><italic>trans</italic>
-acting siRNA</p>
</def>
</def-item>
<def-item><term id="term5">phasiRNA</term>
<def id="def5"><p>phased siRNA</p>
</def>
</def-item>
<def-item><term id="term6">AS</term>
<def id="def6"><p>alignment score</p>
</def>
</def-item>
<def-item><term id="term7">5′-RLM-RACE</term>
<def id="def7"><p>RNA ligation mediated rapid amplification of cDNA ends</p>
</def>
</def-item>
<def-item><term id="term8">PARE</term>
<def id="def8"><p>parallel analysis of RNA ends</p>
</def>
</def-item>
<def-item><term id="term9">Mya</term>
<def id="def9"><p>million years ago</p>
</def>
</def-item>
<def-item><term id="term10">CMS</term>
<def id="def10"><p>cytoplasmic male sterility</p>
</def>
</def-item>
<def-item><term id="term11">IGV</term>
<def id="def11"><p>Integrative Genomics Viewer</p>
</def>
</def-item>
</def-list>
</glossary>
</notes>
</front>
</pmc>
</record>
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